I understand about the amplifier not increasing the actual signal level. I tend to think of it as raising the signal above the noise level to compensate for any signal losses introduced into the installation although that may not be a 100% correct statement.
I was a little confused by seeing such a high level on the meter when measuring the small antenna's amplified signal so I wasn't sure if the meter was seeing the true signal or just everything being raised and it sounds like from what you say it just saw everything raised. What I take from this is that when measuring the actual signal level always measure before any amplification. Since the small antenna had the amplifier built into it I wasn't sure if not powering it up would still put the signal out to the RF connector.
Sounds like from the FCC ruling he should be able to install an antenna above the roof line so I might have him look into that.
I wish I had thought to just go buy another balun since it really seems like that was the real problem but I'm thinking still in theory about the height of the antenna and how much difference getting it above the roof line would make. Now that I think of it, when standing up there I couldn't see over the roof line so I'm thinking the walls are more like 6' tall. But since it such a large area up there wouldn't the signal in the middle of the roof area not be impacted so much by the metal flashing? Here's an exact location so you can see what I'm talking about
http://goo.gl/maps/Kj7h